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Global Engage 6th Microbiome R&D and Business Collaboration Forum Summary: Days 1 & 2

Leaders in the microbiome industry met in San Diego (USA) for two days, on October 29th and 30th, 2018, to dive into the advancements in research and product development that have occurred to date. Microbiome Insights was an exhibitor at this event—The 6th Microbiome R&D and Business Collaboration Forum–one of the largest annual microbiome-related gatherings in the US, with 300 attendees coming from North America and Europe.

The conference talks were divided into three tracks: microbiome therapeutics, skin microbiome, and probiotics. Here, we present highlights from each of the tracks in this two-day event:

Day 1

Probiotics

Jennifer Spinler of Baylor College of Medicine spoke on “Targeting Antibiotic-Associated Digestive Diseases Using Next-Generation Probiotics”. She started by outlining the need for new therapies to prevent antibiotic-associated diarrhea. Clostridium difficile infection is one of the leading reasons for antibiotic administration, and a 2017 Cochrane Review showed probiotics can prevent Clostridium difficile-associated diarrhea in adults and children. Spinler’s approach is to explore a probiotic strategy for preventing Clostridium difficile infection in the first place by looking at how host bacteria are normally able to protect against C. difficile. She focused on Lactobacillus reuteri, which has anti-inflammatory effects and activity against Gram positive and Gram negative bacteria. She found that L. reuteri alone didn’t prevent the growth of C. difficile, but L. reuteri plus glycerol knocked down C. diff growth in the system—with an accompanying shift in the overall microbial community.

Brunella Gonzalez Cautela of Lallemand gave a talk on “Probio’Stick and the brain-gut axis: Focus on recent clinical findings”. She noted that the etiology of depression is obscure, but one contributor under consideration is immune-mediated inflammation. She thus posed the question: can probiotics be used for depression? A pilot study by the company, in collaboration with researchers from Queen’s University, focused on patients who were depressed but never treated before. In addition to completing a survey, the subjects were tested for inflammatory markers in the blood, serotonin levels, and fecal microbiome composition. Those who received ProbioStick for 8 weeks showed significant improvement in mood-related symptoms compared to those who received a placebo.

Microbiome

Kathy McCoy of University of Calgary presented on “Impact of the gut microbiome in shaping innate immunity: Defining Mechanisms”, going over several examples of using gnotobiotics to define mechanisms underlying microbiome and host interactions. In one example, researchers studied microbial impact on T Cells in a non-obese diabetic mouse model of type 1 diabetes. They looked at the ability of the bacteria to bring the integrase-specific T cells to the gut, and found that microbial antigens had a dramatic protective effect against colitis.

Jessica Schneider of Takeda Pharmaceuticals spoke about the company’s growing microbiome drug portfolio, and how gastrointestinal indications are paving the way for future indications (gut-brain axis and others). She explained the company’s interest in commensal bacterial co-occurrence networks in various disease states, and deriving effective therapeutics from these. Takeda is driven by the hypothesized mechanism of disease: either bugs as drugs, or (in the case of their collaboration with Enterome), drugs for/from bugs. She listed approaches in the industry, in increasing order of R&D complexity: fecal microbiota transplantation, bacteriophage engineering, bacterial consortia, engineered bacteria, single strain commensal bacteria, and small molecules.

Morten Isaksen of Bio-Me spoke on “Positioning microbiome analysis for use in precision medicine”. The company has developed a platform that does precision microbiome profiling (species/strain level) and direct quantification reads in less than a day. Isaksen described a demonstration study on diet: subjects consumed their normal diet for 4 weeks, then changed their diet in some way for the next 4 weeks—for example, consuming more fiber or changing sugar consumption. Bio-Me carried out daily sampling of fecal microbiota and found, interestingly, that after an initial microbiome change (after 3-5 days) there tended to be a rebound to pre-intervention levels of bacteria. Follow-up work will try to uncover the cause of this phenomenon.

Skin microbiome

Kausar Malik of Amway Corporation presented “The Cinco de Mayo Study: A one-year longitudinal study of the facial skin microbiome in normal healthy adults”—a project done in collaboration with the Microbiome Insights team. Malik described how bacterial species on the skin vary depending on the environment (e.g. moist or dry); the study aimed to find out the stability of the skin microbiome in a large population of healthy individuals over time, in order to begin identifying biomarkers of skin aging. In addition to skin swabs, they looked at red spots, wrinkles, brown spots, skin elasticity, barrier function, and surface pH. They found no significant change in alpha diversity over time, although some individuals showed a change in microbiome diversity on the cheek. Corynebacterium increased with age, and was also correlated with higher redness (in line with other published work).

Day 2

Microbiome

Eric Pamer of Memorial Sloan Kettering Cancer Center gave a keynote address on “Microbiota-mediated defense against intestinal infection”. His research focused on patients undergoing allogeneic hematopoietic stem cell transplantation (allo-HSCT): these patients receive antibiotics, chemotherapy, and radiation, and mortality is high in the case of bloodstream infection caused by vancomycin-resistant enterococcus (VRE). Given that the microbiome normally eliminates persistent VRE, the question is whether there’s a way to eliminate VRE in allo-HSCT patients. Pamer and colleagues showed that with a fecal transplant in these patients they re-established almost all the normal microbiome components—but which bugs were causing clearance of VRE? The researchers used particular bacteria and did a dilution test to examine the clearance of VRE. Blautia producta were the only bacteria that caused complete inhibition. When they looked into what Blautia producta expresses that none of the others do, they found it encodes a lantibiotic operon; these lantibiotics can also be expressed by anaerobes living in the colon.

Peter Spanogiannopoulos of UCSF was next up, with “The metabolism of fluoropyrimidine anticancer drugs by the human gut microbiome”. He cited work showing that Proteobacteria can inactivate 5FU—and noted that, fortunately, there is a lot about Proteobacteria in literature. He and his colleagues in the Turnbaugh lab are looking to answer the question: can probiotics rescue toxicity? One day they hope to sequence someone’s microbiome before administering anticancer drugs, in order to assess the pharmacokinetics.

Pierre Belichard of Enterome spoke on “Building the leading microbiome-derived immunotherapy company”. He explained that Enterome, a spin-out of MetaGenoPolis in France, is focused on determining function of the microbiome in cancer and inflammatory bowel disease. They are developing everything except ‘live biotics’—and their multiple programs are currently in various stages: for instance, glioblastoma and solid tumors (phase 1); Crohn’s disease (phase 2). They work on epitope mimicry to trigger an anti-tumor T-cell response, ‘waking up’ existing dormant T-cells in the gut lining to activate the biggest group of T cells in the human body. Their work in animal models has established this and they are now carrying it through in clinical trials with humans.

The next event in the microbiome track was a panel discussion led by Microbiome Insights CEO Malcolm Kendall: “Where the money is going and where the money will be made: The unique perspective of venture capitalists”. On the panel were Asish Xavier of J&J Innovation and Denise Kelly of Seventure. In response to an audience question, the panelists emphasized that they look carefully at every company that comes through the door; sometimes they ask for more information or progress and a company comes back later having secured a better position. Kendall asked the panelists the key things they look for in a company, and Kelly responded that the number one factor is top-notch science: validated and preferably peer-reviewed. Then comes intellectual property: who else is competing, and what makes the company different? Third is the business team and the research team. Xavier agreed, adding that the science may be very interesting but the key is whether it is translatable.

Timing is another factor: Xavier says he has seen companies take 20 years to bring something to market. He said timing is critical for a company—so sometimes he explores whether they can build a small product to bring to market while working on a larger one.

Kendall asked the panelists how they think microbiome science is progressing. Xavier acknowledged a lot of good science emerging—with an exponential number of publications—but not all of the ideas can be translated into a drug. The science only has potential as a company if you can get to phase 3 and beyond. Most times the drugs will be advanced by a bigger company because of regulatory challenges so the start-ups will have to partner at some point in their existence. Kelly agreed, and noted that over the past five years we have seen a massive capitalization of the scientific progress.

For more on the conference talks, see #MicrobiomeProbioticsForum on Twitter.

PRESS RELEASE: Rebiotix and Microbiome Insights collaborate on a microbiome IBD tool for clinical development

Recent study provides proof of concept for using novel scoring system to define IBD-related changes in microbiome

With a growing body of science linking gut microbiota to inflammatory bowel disease (IBD), a need exists in clinical settings to understand changes in the gut microbial community as they relate to IBD and its management.
Two leading microbiome companies, Rebiotix (part of the Ferring Pharmaceuticals Group) and Microbiome Insights, are collaborating to validate one such tool: a proprietary analysis to determine how closely a patient’s microbiome resembles that of someone with IBD. Microbiome Insights’ bioinformaticians developed an IBD Microbiome Score, based on a vast dataset of over 1600 individuals with IBD and healthy controls. The metric combines the latest understandings of the gut microbiome as a complex ecosystem with information on hundreds of taxa in the bacterial community, rather than the presence or absence of specific taxa. Based on fecal microbial characterization by sequencing, the IBD Microbiome Score can be assigned for each individual patient at diagnosis and at different times throughout treatment, making the Score practical for clinical use. Leveraging Rebiotix’s proprietary Microbiota Restoration Therapy™ (MRT) drug development platform, the Score is being evaluated in active clinical trials to treat IBD.

“The microbiome field is enormously complex,” says Dr. Ken Blount, Rebiotix’s Chief Scientific Officer. “With the use of the first-in-class Rebiotix MRT platform continuing to expand into complex conditions such as IBD, it is critical to have strong, scientifically-validated tools to understand the dynamics of the microbiomes changes within our patients. We’ve seen first-hand how the novel platform and expertise of Microbiome Insights has the potential to rapidly advance not only our understanding of the impact of MRT on patients, but also to uncover valuable microbiome findings for the entire industry.”

“Our scientific team has consulted with leading gastroenterologists to explore ways of leveraging the science on the microbiome and IBD in the clinical setting,” says Microbiome Insights CEO Malcolm Kendall. “Now we have developed the first scientifically robust tool for tracking the microbiome of people with IBD and understanding its link to clinical outcomes. The ability to work with Rebiotix on this path to discovery underscores the future utility of our platform in the clinical setting.”

The companies are continuing to explore applications of Rebiotix interventions and Microbiome Insights’ personal health platform in other microbiome-related diseases.

About Rebiotix
Rebiotix Inc., part of the Ferring Pharmaceuticals Group, is a late-stage clinical microbiome company focused on harnessing the power of the human microbiome to revolutionize the treatment of debilitating diseases using drug products built on its pioneering Microbiota Restoration Therapy™ (MRT) platform. The MRT platform is a standardized, stabilized drug technology that is designed to rehabilitate the human microbiome by delivering a broad consortium of live microbes into a patient’s intestinal tract via a ready-to-use and easy-to-administer format. For more information on Rebiotix and its pipeline of human microbiome-directed therapies, visit www.rebiotix.com.

About Microbiome Insights
Microbiome Insights, Inc. is a global leader providing end-to-end services for microbiome DNA sequencing, including state-of-the-art bioinformatic analysis. Based in Vancouver, Canada, the company’s customized suite of services enables researchers and clinicians to easily and effectively include microbiome analysis in studies across a range of human, animal, agricultural and environmental applications. The multidisciplinary team of researchers and knowledge leaders at the company provide access to decades of expertise in traditional sciences such as ecology, microbiology, infectious diseases, and genetics. Microbiome Insights’ award-winning team is committed to providing clients with fast, dependable, cost-effective results.

See the original Business Wire press release here.

Denise Kelly representing Seventure on what makes a successful microbiome company

A growing number of start-up microbiome companies—from new players in the established probiotics industry, to university spin-outs focused on novel microbiome-based therapeutics—are looking for support and funding. In this competitive environment, how can a new company make the cut?

For the past several years Professor Denise Kelly has worked with Seventure Partners, a leading European Investor—which has the first venture fund, Health for Life, dedicated to investing in microbiome-focused start-ups, led by Seventure’s CEO, Isabelle de Cremoux. Kelly has participated in panels at both the Translational Microbiome Conference (Boston, USA) and the Global Engage Microbiome Futures event (New York, USA) and recently gave keynote lectures at the IHMC meeting in Killarney and the NeuroCon-X meeting in Prince Edward Island, Canada. Here, Microbiome Insights hears Prof. Kelly’s summary of what will set up a microbiome-based company for success.

Use strong science—and own it

Kelly says Seventure has looked at more than 400 companies in the microbiome sector. The first question she asks is whether the science behind the product or service is robust—a major factor for the Seventure Life Science team. She notes, “We are really fortunate that a lot of interest comes from tier one academics and the findings are published in high-impact journals”—so the science has been peer-reviewed and often validated by independent research, adding to its credibility.

Moreover, Kelly says the strongest scientific ‘package’ combines wetlab work with human studies that address potential mechanisms of action in humans. And she notes that companies generally need to have more than 16S data on hand: “We know so much about strain level impact; shotgun sequencing gets you a lot more information. But even then, the industry is moving towards a multi-omics approach—for example, including metatranscriptomics  and metabolomics, so we know ‘who’ occupies an ecosystem but also what they are doing.”

The next question about the science is whether it’s unique: Do competitors have something similar? Having a strong patent portfolio is crucial as it gives the company a distinct competitive advantage.

Build your revenue stream

Among all the possible life sciences areas in which VCs can invest, microbiome science is still in its early days—meaning they are likely to proceed with caution. Kelly says, “Investing in the ‘discovery’ phase is inherently risky; investors want to see that others have invested in the ideas as well.” She says the solution is to use as many resources as possible to build a company’s revenue space, including building multiple product opportunities and diversifying target disease indications—and importantly, building partnerships and licensing opportunities. Very competitive companies are also winning sizeable non-dilutive grants.

Get your regulatory ducks in a row

The science may look exciting now, but what’s the plan for bringing it to market? Many potential therapeutics in the microbiome area—for example, ‘bugs as drugs’—will face unique regulatory challenges. Kelly recommends connecting with regulatory advisors early on so the company can plan for the realities of getting past the hurdles. And even in cases where the regulatory path for a particular indication is relatively well-established, those at the helm of the company need to understand the complexities of the manufacturing process and how regulatory requirements need to be factored in.

Build relationships strategically

Kelly emphasizes that no successful company is built in a bubble: it needs supporters in order to build success. Companies need relationships with key people in academia and elsewhere—and not just a list of names to put up on the web page, but people who really care about what it’s doing and who are willing to jump in with advice and support.

Kelly says it’s especially important to engage with key opinion leaders (KOLs) with knowledge about the specific indication on which the product is focused. A company that demonstrates authentic engagement with these individuals has a better chance of leading the way in the therapeutic space.

Know when to keep your cards close

As a company is building, it’s important to strategize about how much to reveal—at what times, and to whom. She says, “Approach investors, such as Seventure, when you have a clear vision of your commercial opportunity. Although we invest in early stage start-ups, we appreciate companies that have a strong science package as well as a robust business plan that clearly sells the path to clinic and ultimately, to the marketplace.”

Having all these pieces in place won’t guarantee success—but Kelly says they will certainly make investors take a closer look. “The microbiome industry is moving very fast and the number of new start-ups continues to grow exponentially. At Seventure, we continue to build our portfolio and very recently our CEO, Isabelle de Cremoux, announced the first close of a new AVF fund with Adisseo, dedicated to innovation in Animal Health and Nutrition.”

Without a doubt, the microbiome industry as a whole is truly disruptive and represents a complete paradigm shift in human and animal healthcare. Says Kelly: “We are confronted with numerous modalities, ranging from nutritional products through to microbiome-based drug therapies which can modulate microbiome community function and structure, significantly impacting health status but also disease risk and disease progression. Personalized approaches to medical care are also envisaged, as predictive microbiome biomarkers are being sought—and these could provide more accurate diagnostic and prognostic patient read-outs, leading to more predictable and enhanced drug efficacy. The next five years will be very exciting for many, many reasons. Our knowledge base will continue to grow, but most importantly, we also start to see completion of phase II/III human clinical trials.”

Study led by Afribiota investigators shows stunted growth in children is associated with gastrointestinal ‘de-compartmentalization’

Stunting, the impaired growth and development of children, affects an estimated 155 million children per year. This represents roughly 25% of the world’s children and there exists a substantial lack of knowledge regarding the underlying causes and potential treatments. Current thinking on stunting hypothesizes that contributing factors such as inadequate psychosocial stimulation, poor nutrition, and recurrent infection are to blame. New research, however, is indicating that the microbial community of the small intestine, an organ essential for digestion and nutrient absorption, may be another contributing factor.

New data, published in PNAS by Afribiota investigators, including Microbiome Insights co-founder Dr. Brett Finlay, found that children suffering from stunting are affected by bacterial overgrowth in the small intestine and possess a microbial community made up from mainly oropharyngeal bacteria. Researchers studied duodenal and gastric samples of children with stunting, aged 2-5 years, in comparison with healthy children living in sub-Saharan Africa. Using 16S Illumina amplicon sequencing and semi-quantitative culturing methods they characterized the microbial communities of these children and found the small intestinal bacterial overgrowth in children with stunting.

The small intestines of children with stunting harboured bacterial species normally found in the oropharyngeal cavity. This overgrowth was also represented in fecal samples from the stunted children—which suggested a path toward developing non-invasive biomarkers for this condition. Furthermore, in stunted children Escherichia coli, Shigella species and Campylobacter species were more prevalent and Clostridia, well-known butyrate producers, were reduced.

These results indicate stunted children are experiencing a de-compartmentalization of the gastrointestinal tract, possibly a result of poor oral hygiene, recurrent or chronic rhino-pharyngeal infections, a hypo-chloric environment in the stomach (which weakens the natural barrier of stomach acidity), or other changes to the stomach environment which reduce its ability to kill unwanted bacteria. Importantly, these changes were seen in two geographically and nutritionally distinct populations, providing strong evidence that bacterial overgrowth is a conserved feature of the stunting condition itself.

The exact role of the oropharyngeal bacteria in intestinal inflammation, while yet to be determined, may provide vital information toward understanding the pathophysiology of stunting and potential new treatments.

Vonaesch P, Morien E, Andrianonimiadana L, et al. Stunted childhood growth is associated with decompartmentalization of the gastrointestinal tract and overgrowth of oropharyngeal taxa. Proc Natl Acad Sci U S A. 2018; 155: E8489-E8498.

PRESS RELEASE: Microbiome Insights receives funding from the Government of Canada to develop new microbiome testing platform for managing chronic disease

Vancouver, British Columbia (September 12, 2018)—Microbiome Insights, Inc. is pleased to announce that it will receive a contribution of up to $190,249 from the National Research Council of Canada Industrial Research Assistance Program (NRC IRAP) to help support the development of a new personal health platform of microbiome testing.

Co-founded by Drs. Brett Finlay and Bill Mohn at University of British Columbia in 2015, Microbiome Insights is a rapidly growing company and a global leader in microbiome testing and bioinformatic analysis. The advisory services and financial assistance from the Government of Canada, through NRC IRAP, will help the company expand in a new direction—continuing to develop tools for use in clinical settings as new data emerge on the gut microbiome and health.

“We’re leveraging our expertise in microbiome testing to develop a suite of tools for monitoring chronic disease in clinical practice,” says Microbiome Insights CEO Malcolm Kendall. “From the practitioner interface to the educational components of the test, our team is taking a fresh approach that is going to change the game for microbiome testing.”

The primary aim of the company’s personal health platform is to help address the challenges both healthcare practitioners and individuals face in the management of chronic disease.  Microbiome monitoring in those with chronic disease may provide a tool for assessing response to therapies or to various lifestyle changes (including diet), particularly when integrated with robust research findings and ongoing data collection.

The company’s new testing platform will be aimed at health practitioners helping individuals who live with inflammatory bowel disease. The efforts are led by Nataša Jovic, MBA, who brings to the company twenty years of experience in therapeutic and diagnostic commercialization. The company is currently exploring opportunities to commercialize its platform of microbiome tests for healthcare practitioners through research collaborations and distribution or joint commercialization efforts.

See the original BusinessWire press release here.

New paper from Microbiome Insights co-founder on critical window for the gut microbiome in infants and the later occurrence of asthma

Among serious and chronic childhood diseases, asthma is the most prevalent. Currently there exists no cure for asthma—only treatments designed to help manage symptoms. Recently, a body of research attempting to unravel how this condition develops  in young children has emerged, so that prevention may one day eliminate or reduce the burden of this chronic condition.

Recent work identified the existence of a critical window during the early lives of both mice and children, during which gut microbial changes are associated with the development of asthma. This provided an avenue to explore the role of the gut microbiome during early childhood development and the onset of chronic diseases like asthma. Importantly though, we know the gut microbiome varies greatly among those raised in different geographic regions. Therefore, understanding how changes in gut microbiota related to asthma development differ globally may provide valuable insights into the mechanism of asthma development.

A new paper, led by Microbiome Insights co-founder Brett Finlay and published in The Journal of Allergy and Clinical Immunology, evaluated the associations of fungal and bacterial changes (dysbiosis) in infants raised in the non-industrialized setting of rural Ecuador. The research was conducted as a collaboration between members of the Universities of British Colombia and Calgary, the BC Children’s Hospital, and Universidad Internacional del Ecuador. Children with atopic wheeze (27 in total) along with 70 healthy controls were identified and their bacterial and eukaryotic gut microbiota analysed at age 3 months. Stool samples were collected and sequencing of the 16S and 18S regions predicted bacterial metagenomes while fecal short chain fatty acids were determined via gas chromatography.

Results indicated that, similar to the previous findings in Canadian children, microbial dysbiosis in Ecuadorian infants at 3 months was associated with the subsequent development of atopic wheeze. Surprisingly though, the dysbiosis observed in Ecuador involved different bacteria taxa as well as some fungal species, and this was more pronounced than in Canada. Some predictions based on the metagenome analysis also emphasized significant dysbiosis-associated differences in genes involved in carbohydrate and taurine metabolism. The fecal short-chain fatty acid acetate was reduced while caproate was increased in children at 3 months who later developed atopic wheeze.

This work continues to provide evidence that there is a critical window during the first 100 days of life during which microbial dysbiosis is strongly associated with development of atopic wheeze. The study also yielded several valuable pieces of information. Despite the involvement of different bacteria taxa, both the Canadian and Ecuadorian populations had decreased fecal acetate, suggesting alterations to fermentation patterns may be a common factor associated with atopic wheeze. Furthermore, the pronounced role of fungal dysbiosis in this study led researchers to recommend that “the role of P. kudriavzevii and other yeasts should be explored in mechanistic studies using animal models.”

Along with more studies characterizing the early microbiome in more communities around the world, optimized biomarker studies of microbial taxa and metabolites could lead to better predictions of risk and therapeutic strategies to restore gut microbial health as a prevention method.

 

How Microbiome Insights can help with your Canadian microbiome research grant application

Competition for funding can be tough—but if you’re applying to a Canadian granting agency to fund a microbiome study, the Microbiome Insights team will be pleased to help. Some granting agencies require you to name an industry partner—and as the leading Canadian industry partner dedicated to microbiome testing and bioinformatic analysis, we are positioned to help your application be as successful as possible.

Here are some frequently asked questions about how we can help with microbiome research grant applications in Canada.

What kinds of testing does Microbiome Insights do?

Microbiome insights has a full suite of sequencing options—some of which may not be readily available at your own institution. Our services include amplicon sequencing (16S V4, 16S V1-V3, 16S V4_skin, 18S, ITS2 and Archaeal V4-V5), shotgun metagenomics, and bacterial whole genome sequencing; in addition to sequencing we run short-chain fatty acid analyses and calprotectin testing. If these are relevant to your research, please contact us to for more information on pricing, turnaround time, and support. Feel free to include our details in your grant application to show you’ve got everything lined up and ready to go for your research.

How flexible are the services?

While an end-to-end service is appealing to some, it doesn’t suit everyone. We can provide the full end-to-end service if needed or we can provide only the parts that make sense to you: for example, if you’re interested in learning more about bioinformatics yourself, you can obtain raw data from our team and explore the data on your own. Under this model, you’ll be able to leverage our wet lab standards while continuing to grow your own understanding of the microbiome.

Everything we do it price sensitive, so we have the ability charge per sample rather than having you lock into a full plate or a full run.

How can partnering with Microbiome Insights make the grant application stronger?

Including us in your grant applications shows you have strong collaborators and leading expertise on your side, bridging to the knowledge of our team and our co-founders (Drs. Brett Finlay and Bill Mohn). Through us, you’ll be able to secure expertise and support in the areas where you need it, and you’ll be able to access industry standards and proven pipelines. Moreover, you can be assured that all of this is done in Canada, with leading Canadian experts in the field.

What specific assistance can the Microbiome Insights team offer for grant applications?

We’ll consult with you to better understand (and draft, if necessary) the study design. We can give you guidelines on collection and transport to insert into your application, and can provide a mock report of the results if required. Our team members can also be hired to write a detailed results or methods section for your application.

Most importantly, we also offer a letter of support which details your study objectives, our deliverables for services and reporting, along with workflows and pricing. These details are key features of your submission, and we are always able to edit the details as funding is released.

How many Microbiome Insights clients come from academia?

The majority of our clients at present come from academia and publish their results in leading journals. If you choose to partner with us, you’ll have access to the same exceptional team that’s used by well-known researchers worldwide.

Contact us today using the form below!

On World Microbiome Day, Here Are Ten Microbiome Thought Leaders You Need to Know

Day in and day out, the Microbiome Insights team is immersed in scientific work on the microbiome. But on this very first World Microbiome Day, we’re taking a moment to step back and consider what—and who—made this remarkable field what it is today.

Although microbiome science is relatively young, the newest discoveries are only possible because of the preceding decades of research in fields as diverse as microbiology, genomics, molecular genetics, infectious diseases, and ecology. In this way, every microbiome researcher stands on the shoulders of those who came before.

With the help of Microbiome Insights co-founders Dr. Brett Finlay (Professor of Biochemistry and Molecular Biology, and Microbiology and Immunology at the University of British Columbia) and Dr. Bill Mohn (Professor of Microbiology and Immunology at the University of British Columbia), and our Scientific Advisory Board member Dr. Janet Jansson (Division Director of Biological Sciences at the Pacific Northwest National Laboratory)—all of whom qualify as thought leaders in their own right—we’ve compiled a list of ten scientists who have built a foundation for today’s microbiome researchers. These are individuals who, through their hard work and vision, have inspired their contemporaries to think differently and, in doing so, have shaped the field of microbiome science into what it is today.

Carl Woese

Dr. Carl Woese (1928-2012) was a biophysicist turned evolutionary microbiologist whose influence on the microbiome field cannot be understated. He was the first to show that bacteria evolve—and he demonstrated the phylogenetic relationships that backed this claim. Through this work he redefined the taxonomic scheme used to describe all forms of life on Earth and introduced us to the three domains of life we recognize today: Bacteria, Archaea and Eukaryota. His legacy is still seen in state-of-the-art lab techniques today, as he established phylogenetic methods using small subunit RNA and culture-independent methods that allow researchers to characterize microbial communities without first culturing them.

Norman Pace & trainees, including David Stahl

Dr. Norm Pace is, among many other things, a Distinguished Professor of Molecular, Cellular and Developmental Biology at the University of Colorado as well as a member of the National Academy of Sciences, a Fellow of the American Association for the Advancement of Science, the American Academy of Microbiology, and the American Academy of Arts and Sciences. His distinguished research career began with the breakthrough idea that, rather than trying to culture all of the unknown microbes of the world, one can instead scoop up genes from the environment and sequence them—essentially creating the many areas of microbiome study that are now among the most active in biology. Many trainees of his lab have gone on to make major contributions to many microbiome areas—in particular, Dr. David Stahl with his unique application of microbial ecology to environmental engineering.

James Tiedje

Dr. James Tiedje is a pioneer in the molecular exploration of soil and non-human environments. His work was instrumental in advancing many fields of microbiome research and addresses environmental concerns like climate change and bioremediation. His expertise in the field was even used for space exploration, as he designed experiments for the Viking Rover aimed at finding life on Mars. He is now a Distinguished Professor of Microbiology and Molecular Genetics and of Plant, Soil and Microbial Sciences as well as the Director of the Center for Microbial Ecology at Michigan State University.

Maria Gloria Dominguez-Bello

Dr. Maria Gloria Dominguez-Bello is Research Professor in the Department of Medicine at New York University whose work spans the fields of microbiology, anthropology, and agriculture. Collecting data from different populations across the globe, including populations in remote geographical areas, her work has focused on the immune and metabolic functioning of the microbiota through development, and how modern practices might impact this functioning. She is well known for her pioneering research on how Caesarean section birth impacts infant microbiome development, and possible microbiome ‘restoration’ techniques.

Martin Blaser

Dr. Blaser is Director of the New York University (NYU) Human Microbiome Program, and Professor of Microbiology at NYU School of Medicine. His early work with Helicobacter pylori confirmed its role in diseases like gastric cancer, providing one of the first examples for a bacterial role in these human diseases. He also brought attention to the importance of the early life microbiome and the dangers of antibiotics to a healthy microbiome and drug resistance—concepts covered for the general public in his highly praised book, Missing Microbes.

Jeff Gordon

How does the gut microbiome develop after birth, and how might this affect one’s nutritional status? These are the questions that drive Dr. Jeff Gordon, the Dr. Robert J. Glaser Distinguished University Professor at Washington University in St. Louis. He has shone a light on the role of the gut microbiota in metabolism and has taken on two pressing global health challenges: obesity and childhood malnutrition. By exploring interactions between the diet and gut microbiome he is discovering potential new ways of optimizing gut community development during the first few years of life.

Patrick Schloss

Dr. Patrick Schloss, now Professor in the Department of Microbiology and Immunology at the University of Michigan, took an interest in bacteria early in his career—not only the bacteria present in samples, but also what they were doing there. To answer this, he used gene sequencing and developed critical tools for analyzing microbiome data and making the interpretation of this data more accurate. With his flair for bioinformatics, his work has helped others make sense of the vast amounts of data generated by microbiome studies.

Stanley Hazen

Dr. Stan Hazen, chair of the Department of Cellular & Molecular Medicine in the Lerner Research Institute at Cleveland Clinic, changed the way researchers think about diet, the gut microbiome, and heart diseases by showing for the first time that a microbial metabolite (TMAO) was linked to cardiovascular disease. With his groundbreaking work in atherosclerosis and inflammatory disease research, he has impacted clinical practice and has laid the foundation for FDA-cleared diagnostic tests and cardiovascular disease drug development. Among his many accolades is his recognition as 2017 Distinguished Scientist by The American Heart Association for his many contributions to the field.

Eran Elinav

After completing his medical specialization as a doctor of internal medicine, Dr. Eran Elinav moved to the Department of Immunology at the Weizmann Institute in Israel. His work has uncovered the very personal links between humans, their diet, and gut bacteria. This has led to microbiome-focused research on personalized physiological responses to nutrition, and has garnered him several accolades including The Rappaport Prize for Excellence in the field of Biomedical Research.

Highlights of the Microbiome Drug Development Summit 2018 in Boston

Development and commercialization of microbiome-based therapeutics was the focus of a recent event in Boston (USA): the Microbiome Drug Development Summit 2018, organized by Hanson Wade. The Microbiome Insights team was in attendance – and here we share some of the highlights from this exciting event:

DAY 1

Jennifer Wortman, Senior Director, Bioinformatics, Seres Therapeutics

Unraveling Microbiome Signatures for Drug Design

Seres Therapeutics, one of the top 5 microbiome biotechnology companies in the world by funding, has a robust microbiome development pipeline. Their approach for addressing disease is to supply bacterial species that are associated with health in an attempt to change disease course.

Wortman explained the company has an extensive strain library isolated from healthy donors. They design consortia for their treatments using in silico design models (e.g. species and functions to reduce inflammation and increase epithelial barrier integrity) and by looking at species that are naturally co-occurring.

One product, SER-287, is an orally delivered community of purified Firmicutes spores associated with gastrointestinal health; it has efficacy in mild to moderate ulcerative colitis and is currently in phase 2B clinical trials. No serious drug-related adverse effects were noted in the trials. Research on SER-287 looks at engraftment: which species were absent at baseline but present after treatment? In all groups, they have seen engraftment of the spore-forming species following treatment: 19 species were more prevalent in patients achieving clinical remission; 13 species were more prevalent in patients not achieving remission.

Julia Cope, Director Scientific Operations, Diversigen

Microbiome Tools and Trends for the Pharmaceutical Industry

Cope spoke about the process for developing drugs to address various microbiome-linked diseases, including obesity, IBD, and cancer. To treat a disease, you need to know what to target. She cautioned that not all targets are likely to be bacterial in origin; researchers should also pay attention to viruses or fungal members of the microbiota.

Cope gave an example of four different studies that revealed four different microbiome-disease associations: taxonomy was similar but the specific biomarkers were different. She advised integrating as many cohorts as possible in order to prevent confounds.

Cathryn Nagler, President ClostraBio & Professor, University of Chicago

The Gut Microbiome, Immunity, and Allergic Disease

Nagler’s central question was whether we’ll be able to develop new microbiota-based strategies to regulate or prevent food allergies. She explained that certain populations of bacteria (classified as clostridia) make barrier-protective cytokines; they also stimulate the production of mucus, antibacterial peptides, etc.

Nagler’s data showed that lactobacilli were depleted in infants allergic to cow’s milk, with an increase in microbes that typically characterize an adult microbiome. Treatment with LGG increased tolerance of cow’s milk in these infants, and increased fecal butyrate. ClostraBio is engineering synthetic drugs to mimic the protective function of the health-associated bacteria.

Mark Smith, CEO Finch Therapeutics Group

Leveraging Reverse Translation to Develop Microbial Therapies

Smith described how broad-spectrum microbial interventions (i.e. fecal microbiota transplantation, or FMT) have good safety profiles in different therapeutic areas. Finch is using data from FMT trials to identify the bacteria linked with positive clinical outcomes, and then making these into bacterial cocktails for the treatment of disease. Smith described their product FIN-524 (developed with Takeda)–noting the challenges in understanding which organisms are driving the response.

An afternoon panel discussion, called Clinical Development of Microbiome-Based Therapeutics, covered a range of questions: clinical trial design in the development of microbiome-based therapeutics; key learnings from existing clinical programs for these therapeutics; and the relative importance of clinical efficacy and mechanism of action.

The panel discussed ‘hype’ in the media: some outlets inflate the importance of the scientific results, but companies need to temper the enthusiasm and stay focused on robust science. As for health professionals, they may be aware of this area but they are uncomfortable talking to patients about it until new products are approved and released into the market.

Regulation was another topic of interest: in particular, the need for flexibility in regulating new microbiome-related drugs. Panelists noted that there’s very little guidance in both the US and Europe, and it might make sense to develop guidelines or have guidance to expedite the development of some of these products. The Parallel Scientific Review is one mechanism that could help.

DAY 2           

Evgueni Doukhanine, R&D Scientist, Microbiome, DNA Genotek

Establishing Techniques for Reproducible and Insightful Microbiome Studies

Doukhanine discussed the necessary steps to design microbiome studies for scalability and innovative analysis. Many people pay attention to the sequencing technology—but the bioinformatics pipeline is also a very important factor. For 16S, they have seen that depending on the bioinformatic pipeline, the relative abundance recovery is quite different. DNA Genotek has moved from collection kits into study design consultation.

Phil Strandwitz, Co-founder & CEO, Holobiome

GABA-Modulating Bacteria of the Human Gut Microbiota

Strandwitz gave an overview of the microbiota-gut-brain axis and described the identification of a bacterium from the human microbiota that’s completely dependent on GABA for growth; Holobiome is using it to identify and culture a panel of diverse GABA-producing bacteria with the hopes that they can modulate levels of this important neurotransmitter.

Microbiome Insights to mark opening of new lab space with champagne reception and microbiome poster competition

Microbiome Insights, Inc. is planning to move operations into a new laboratory space in UBC’s Pharmaceutical Sciences building — and to mark the occasion, they will host a champagne reception with a poster competition open to local microbiome researchers.

Poster competition details:

The competition is open to all researchers and research assistants affiliated with UBC. Participants may bring any poster related to microbiome data collected within the past five years — up to 3 posters per participant may be entered.

Posters previously presented at academic conferences are encouraged! Most standard poster sizes can be accommodated.

Posters will be judged on both scientific content and presentation. Judges will award first, second, and third prizes as well as a “crowd favourite”.

DATE: Monday, May 28th, 2018

TIME: 4:00 pm to 6:00 pm

PLACE: Pharmaceutical Sciences Building, UBC Campus (2405 Wesbrook Mall, Vancouver, V6T 1Z3), Mezzanine floor

Participants should bring their poster for setup between 1:00 and 3:30 on May 28th. Winners will be announced during the champagne reception at 5:30.

Prizes are as follows:

First place: 50 free samples of amplicon sequencing ($5,500 value)
Second place: 30 free samples of amplicon sequencing ($3,300 value)
Third place: 20 free samples of amplicon sequencing ($2,200 value)
Crowd favourite: Cash prize of $250

RSVP for the poster competition to Jen Bower: jbower1023@gmail.com

Only the first 30 entries can be accepted, so email now!

 

 

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